quite confuzzled into thinking I understand something when I really don't. BUT- for what it's worth, here is my understanding:

FM goes through a series of remissions and exacerbations, meaning symptoms less apparent and symptoms more apparent. The times when FM is more apparent, or disabling, are flares.

Breakthrough pain is when you are taking your 'regular' pain relief medication- whether it be tylenol, Tramadol, or Morphine, and are still experiencing disabling symptoms (pain). It is for those times that a doc will often prescribe another, different class usually, pain Rx.